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cellxgene-skill

Submit compact CELLxGENE Discover API requests for public collection and dataset metadata. Use when a user wants concise single-cell collection summaries

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--cellxgene-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/cellxgene-skill/SKILL.md -o .claude/skills/cellxgene-skill.md

Drops the SKILL.md into .claude/skills/cellxgene-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

Operating rules

  • Use scripts/rest_request.py for all CELLxGENE Discover calls.
  • Use base_url=https://api.cellxgene.cziscience.com/curation/v1.
  • Prefer targeted collection detail lookups rather than full archive dumps by default.
  • The public collections list can be large and may require a higher timeout_sec; collection detail lookups are usually the better first call.
  • Re-run requests in long conversations instead of relying on older tool output.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return raw JSON only if the user explicitly asks for machine-readable output.
  • Prefer these paths: collections/<collection_id> first, then collections when the user explicitly wants broad archive discovery.

Input

  • Read one JSON object from stdin.
  • Required fields: base_url, path
  • Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
  • Common CELLxGENE patterns:
    • {"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}
    • {"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections","timeout_sec":60,"max_items":5}

Output

  • Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
  • Use raw_output_path when save_raw=true.
  • Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://api.cellxgene.cziscience.com/curation/v1","path":"collections/db468083-041c-41ca-8f6f-bf991a070adf","max_items":5}' | python scripts/rest_request.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.